1. S. Ferré and R. D. King. A dichotomic search algorithm for mining and learning in domain-specific logics. Fundamenta Informaticae -- Special Issue on Advances in Mining Graphs, Trees and Sequences, 66:1-32, 2005. [PDF] Keyword(s): logic functors, data-mining, concept analysis, logic, machine learning. Abstract:

   Many application domains make use of specific data structures such as sequences and graphs to represent knowledge. These data structures are ill-fitted to the standard representations used in machine learning and data-mining algorithms: propositional representations are not expressive enough, and first order ones are not efficient enough. In order to efficiently represent and reason on these data structures, and the complex patterns that are related to them, we use domain-specific logics. We show these logics can be built by the composition of logical components that model elementary data structures. The standard strategies of top-down and bottom-up search are ill-suited to some of these logics, and lack flexibility. We therefore introduce a dichotomic search strategy, that is analogous to a dichotomic search in an ordered array. We prove this provides more flexibility in the search, while retaining completeness and non-redundancy. We present a novel algorithm for learning using domain specific logics and dichotomic search, and analyse its complexity. We also describe two applications which illustrates the search for motifs in sequences; where these motifs have arbitrary length and length-constrained gaps. In the first application sequences represent the trains of the East-West challenge; in the second application they represent the secondary structure of Yeast proteins for the discrimination of their biological functions.

   
   

   @article{FerKin2004b,
   author = {Ferré, S. and King, R. D.},
   title = {A dichotomic search algorithm for mining and learning in domain-specific logics},
   journal = {Fundamenta Informaticae -- Special Issue on Advances in Mining Graphs, Trees and Sequences},
   volume = {66},
   number = {},
   pages = {1--32},
   year = {2005},
   publisher = {IOS Press},
   pdf = {http://www.irisa.fr/LIS/ferre/papers/fi-mgts2004.pdf},
   abstract = { Many application domains make use of specific data structures such as sequences and graphs to represent knowledge. These data structures are ill-fitted to the standard representations used in machine learning and data-mining algorithms: propositional representations are not expressive enough, and first order ones are not efficient enough. In order to efficiently represent and reason on these data structures, and the complex patterns that are related to them, we use domain-specific logics. We show these logics can be built by the composition of logical components that model elementary data structures. The standard strategies of top-down and bottom-up search are ill-suited to some of these logics, and lack flexibility. We therefore introduce a dichotomic search strategy, that is analogous to a dichotomic search in an ordered array. We prove this provides more flexibility in the search, while retaining completeness and non-redundancy. We present a novel algorithm for learning using domain specific logics and dichotomic search, and analyse its complexity. We also describe two applications which illustrates the search for motifs in sequences; where these motifs have arbitrary length and length-constrained gaps. In the first application sequences represent the trains of the East-West challenge; in the second application they represent the secondary structure of Yeast proteins for the discrimination of their biological functions.},
   keywords = {logic functors, data-mining, concept analysis, logic, machine learning},
   
   }
   

1. S. Ferré, O. Ridoux, and B. Sigonneau. Arbitrary Relations in Formal Concept Analysis and Logical Information Systems. In ICCS, LNCS 3596, pages 166-180, 2005. Springer. [PDF] Keyword(s): navigation, logical information system, relation, logical concept analysis. Abstract:

   A logical view of formal concept analysis considers attributes of a formal context as unary predicates. In a first part, we propose an augmented definition that handles {\em binary relations} between objects. A Galois connection is defined on augmented contexts. It represents concept inheritance as usual, but also relations between concepts. As usual, labeling operators are also defined. In particular, concepts and relations are visible and labeled in a single structure. In a second part, we show how relations can be used for navigating in an augmented concept lattice. This part augments the theory of Logical Information Systems. An implementation is sketched, and first experimental results are presented.

   
   

   @inproceedings{FerRidSig2005,
   author = {Ferré, S. and Ridoux, O. and Sigonneau, B.},
   title = {Arbitrary Relations in Formal Concept Analysis and Logical Information Systems},
   booktitle = {ICCS},
   year = {2005},
   pages = {166-180},
   publisher = {Springer},
   series = {LNCS 3596},
   abstract = {A logical view of formal concept analysis considers attributes of a formal context as unary predicates. In a first part, we propose an augmented definition that handles {\em binary relations} between objects. A Galois connection is defined on augmented contexts. It represents concept inheritance as usual, but also relations between concepts. As usual, labeling operators are also defined. In particular, concepts and relations are visible and labeled in a single structure. In a second part, we show how relations can be used for navigating in an augmented concept lattice. This part augments the theory of Logical Information Systems. An implementation is sketched, and first experimental results are presented.},
   pdf = {http://www.irisa.fr/LIS/ferre/papers/iccs2005.pdf},
   keywords = {navigation, logical information system, relation, logical concept analysis},
   
   }
   




2. Y. Padioleau, B. Sigonneau, O. Ridoux, and S. Ferré. LISFS: a Logical Information System as a File System. In Véronique Benzaken, editor, Bases de données avancées, pages 393-398, October 2005. Université de Rennes 1. [PDF] Keyword(s): databases, logical file system, logical information system. Abstract:

   We present Logical Information Systems (LIS). A LIS can be viewed as a schema-less database whose objects are described by logical formulas. Objects are automatically organized according to their logical description, and logical formulas can be used for representing both queries and navigation links. The key feature of a LIS is that it answers a query with a set of navigation links expressed in the same logic as the query. As navigation links are dynamically computed from any query, and can be used as query increments, it follows that querying and navigation steps can be combined in any order. We then present LISFS, a file-system implementation of a LIS, where objects are files or parts of files. This has the benefit to make LIS features available right now to existing applications. This implementation can easily be extended and specialized through a plug-in mechanism. Finally, we present some applications in the field of personal databases (e.g., music, images, emails), and demonstrate that building specialized interfaces for visualizing databases can be done easily through LISFS navigation.

   
   

   @inproceedings{PSRF2005,
   author = {Padioleau, Y. and Sigonneau, B. and Ridoux, O. and Ferré, S.},
   title = {LISFS: a Logical Information System as a File System},
   booktitle = {Bases de données avancées},
   pages = {393--398},
   year = {2005},
   editor = {Benzaken, Véronique},
   month = {oct},
   publisher = {Université de Rennes 1},
   pdf = {http://www.irisa.fr/LIS/sigonneau/publications/articles/bda2005.pdf},
   abstract = {We present Logical Information Systems (LIS). A LIS can be viewed as a schema-less database whose objects are described by logical formulas. Objects are automatically organized according to their logical description, and logical formulas can be used for representing both queries and navigation links. The key feature of a LIS is that it answers a query with a set of navigation links expressed in the same logic as the query. As navigation links are dynamically computed from any query, and can be used as query increments, it follows that querying and navigation steps can be combined in any order. We then present LISFS, a file-system implementation of a LIS, where objects are files or parts of files. This has the benefit to make LIS features available right now to existing applications. This implementation can easily be extended and specialized through a plug-in mechanism. Finally, we present some applications in the field of personal databases (e.g., music, images, emails), and demonstrate that building specialized interfaces for visualizing databases can be done easily through LISFS navigation. },
   keywords = {databases, logical file system, logical information system},
   
   }
   

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